BioC 2.13: CHECK report for edgeR on perceval

Package: edgeR

Version: 3.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_3.4.2.tar.gz

StartedAt: 2014-04-05 01:03:08 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:04:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 101.1 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/edgeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.4.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘edgeR’ can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘edgeR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’ [7s/8s]
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 [8s/8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/edgeR.Rcheck/00check.log’
for details.

* installing *source* package ‘edgeR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_loess_by_col.cpp -o R_loess_by_col.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_cr_adjust.cpp -o R_cr_adjust.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_one_group.cpp -o R_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c core/adj_coxreid.cpp -o core/adj_coxreid.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c core/glm_levenberg.cpp -o core/glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c core/glm_one_group.cpp -o core/glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c core/interpolator.cpp -o core/interpolator.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I.  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c core/fmm_spline.c -o core/fmm_spline.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.049	0.002	0.052
WLEB	0.235	0.011	0.249
adjustedProfileLik	0.022	0.002	0.024
aveLogCPM	0.015	0.000	0.016
binomTest	0.012	0.001	0.012
calcNormFactors	0.014	0.001	0.015
camera.DGEList	0.355	0.021	0.379
commonCondLogLikDerDelta	0.015	0.000	0.017
condLogLikDerSize	0.008	0.000	0.009
cpm	0.013	0.001	0.015
cutWithMinN	0.009	0.001	0.010
dglmStdResid	0.085	0.006	0.093
dim	0.016	0.001	0.017
dispBinTrend	0.822	0.008	0.840
dispCoxReid	0.047	0.001	0.048
dispCoxReidInterpolateTagwise	0.050	0.003	0.053
dispCoxReidSplineTrend	0.984	0.013	1.011
edgeRUsersGuide	0.019	0.002	0.022
equalizeLibSizes	0.033	0.001	0.037
estimateCommonDisp	0.039	0.001	0.040
estimateDisp	0.336	0.006	0.347
estimateExonGenewisedisp	0.036	0.001	0.038
estimateGLMCommonDisp	0.123	0.001	0.127
estimateGLMTagwiseDisp	0.250	0.006	0.268
estimateGLMTrendedDisp	0.210	0.005	0.218
estimateTagwiseDisp	0.005	0.000	0.005
estimateTrendedDisp	0.826	0.024	0.871
exactTest	0.032	0.001	0.034
expandAsMatrix	0.006	0.001	0.005
getCounts	0.020	0.001	0.020
getPriorN	0.008	0.000	0.008
glmfit	0.174	0.002	0.177
gof	0.032	0.001	0.033
goodTuring	0.016	0.001	0.016
loessByCol	0.008	0.001	0.008
maPlot	0.023	0.002	0.025
maximizeInterpolant	0.009	0.001	0.009
maximizeQuadratic	0.009	0.000	0.009
meanvar	0.092	0.004	0.098
mglm	0.064	0.001	0.067
movingAverageByCol	0.102	0.000	0.103
plotBCV	0.729	0.013	0.761
plotExonUsage	0.018	0.001	0.021
plotMDS.DGEList	0.044	0.002	0.048
plotSmear	0.543	0.006	0.570
predFC	0.039	0.001	0.049
q2qnbinom	0.091	0.002	0.097
readDGE	0.004	0.001	0.005
roast.DGEList	0.268	0.006	0.277
spliceVariants	0.032	0.002	0.035
splitIntoGroups	0.016	0.001	0.017
subsetting	0.066	0.002	0.069
systematicSubset	0.008	0.000	0.008
thinCounts	0.008	0.001	0.007
topTags	0.048	0.002	0.049
weightedCondLogLikDerDelta	0.012	0.001	0.015
zscoreNBinom	0.006	0.000	0.006